The decision to attack the center "was undertaken in 1993 by the highest authorities of the then-government of," prosecutor Alberto Nisman said at a news conference.
He said the actual attack was entrusted to the Lebanon-based group Hezbollah.
The worst terrorist attack ever on Argentine soil, the bombing of the Jewish cultural center in Buenos Aires killed 85 people and injured more than 200 when an explosive-laden vehicle detonated near the building.
Iran's government has vehemently denied any involvement in the attack following repeated accusations by Jewish community and other leaders here.
Prosecutors urged the judge to seek international and national arrest orders for Rafsanjani, who was Iran's president between 1989 and 1997.
They also were asking the judge to detain several other former Iranian officials, including a former intelligence chief, Ali Fallahijan, and former Foreign Minister Ali Ar Velayati.
They also said they were urging the judge to order the arrest of two former commanders of Iran's Revolutionary Guards, two former Iranian diplomats and a former Hezbollah security chief for external affairs.
Nisman and fellow prosecutor Marcelo Martinez Burgo said they suspected that Hezbollah undertook activities outside Lebanon only "under orders directly emanating from the regime in Tehran."
That could be a problem for Iran right now if the judge requests international warrants.